scholarly journals Spatial organization of endometrial gene expression at the onset of embryo attachment in pigs

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shuqin Zeng ◽  
Susanne E. Ulbrich ◽  
Stefan Bauersachs
Keyword(s):  
Gene Expression ◽  
Blood Vessels ◽  
Growth Regulation ◽  
Spatial Organization ◽  
Interleukin 1 ◽  
Differential Expression Analysis ◽  
Cell Types ◽  
Cell Junction ◽  
Endometrial Cell ◽  
Filamentous Form

Abstract Background During the preimplantation phase in the pig, the conceptus trophoblast elongates into a filamentous form and secretes estrogens, interleukin 1 beta 2, interferons, and other signaling molecules before attaching to the uterine epithelium. The processes in the uterine endometrium in response to conceptus signaling are complex. Thus, the objective of this study was to characterize transcriptome changes in porcine endometrium during the time of conceptus attachment considering the specific localization in different endometrial cell types. Results Low-input RNA-sequencing was conducted for the main endometrial compartments, luminal epithelium (LE), glandular epithelium (GE), blood vessels (BV), and stroma. Samples were isolated from endometria collected on Day 14 of pregnancy and the estrous cycle (each group n = 4) by laser capture microdissection. The expression of 12,000, 11,903, 11,094, and 11,933 genes was detectable in LE, GE, BV, and stroma, respectively. Differential expression analysis was performed between the pregnant and cyclic group for each cell type as well as for a corresponding dataset for complete endometrium tissue samples. The highest number of differentially expressed genes (DEGs) was found for LE (1410) compared to GE, BV, and stroma (800, 1216, and 384). For the complete tissue, 3262 DEGs were obtained. The DEGs were assigned to Gene Ontology (GO) terms to find overrepresented functional categories and pathways specific for the individual endometrial compartments. GO classification revealed that DEGs in LE were involved in ‘biosynthetic processes’, ‘related to ion transport’, and ‘apoptotic processes’, whereas ‘cell migration’, ‘cell growth’, ‘signaling’, and ‘metabolic/biosynthetic processes’ categories were enriched for GE. For blood vessels, categories such as ‘focal adhesion’, ‘actin cytoskeleton’, ‘cell junction’, ‘cell differentiation and development’ were found as overrepresented, while for stromal samples, most DEGs were assigned to ‘extracellular matrix’, ‘gap junction’, and ‘ER to Golgi vesicles’. Conclusions The localization of differential gene expression to different endometrial cell types provided a significantly improved view on the regulation of biological processes involved in conceptus implantation, such as the control of uterine fluid secretion, trophoblast attachment, growth regulation by Wnt signaling and other signaling pathways, as well as the modulation of the maternal immune system.

scholarly journals Identifying inaccuracies in gene expression estimates from unstranded RNA-seq data

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mikhail Pomaznoy ◽  
Ashu Sethi ◽  
Jason Greenbaum ◽  
Bjoern Peters
Keyword(s):  
Gene Expression ◽  
Differential Expression Analysis ◽  
Cell Types ◽  
Library Preparation ◽  
Rna Seq ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Machine Learning Model ◽  
Specific Manner ◽  
Library Preparation Protocol

Abstract RNA-seq methods are widely utilized for transcriptomic profiling of biological samples. However, there are known caveats of this technology which can skew the gene expression estimates. Specifically, if the library preparation protocol does not retain RNA strand information then some genes can be erroneously quantitated. Although strand-specific protocols have been established, a significant portion of RNA-seq data is generated in non-strand-specific manner. We used a comprehensive stranded RNA-seq dataset of 15 blood cell types to identify genes for which expression would be erroneously estimated if strand information was not available. We found that about 10% of all genes and 2.5% of protein coding genes have a two-fold or higher difference in estimated expression when strand information of the reads was ignored. We used parameters of read alignments of these genes to construct a machine learning model that can identify which genes in an unstranded dataset might have incorrect expression estimates and which ones do not. We also show that differential expression analysis of genes with biased expression estimates in unstranded read data can be recovered by limiting the reads considered to those which span exonic boundaries. The resulting approach is implemented as a package available at https://github.com/mikpom/uslcount.

scholarly journals Local translation in synaptic mitochondria influences synaptic transmission

2020 ◽  
Author(s):  
Roya Yousefi ◽  
Eugenio F. Fornasiero ◽  
Lukas Cyganek ◽  
Stefan Jakobs ◽  
Silvio O. Rizzoli ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hippocampal Neurons ◽  
Spatial Organization ◽  
Mitochondrial Gene ◽  
Cell Types ◽  
Synaptic Function ◽  
Synaptic Activity ◽  
Mitochondrial Gene Expression ◽  
Mitochondrial Translation ◽  
Ample Evidence

ABSTRACTMitochondria possess a small genome that codes for core subunits of the oxidative phosphorylation system, and whose expression is essential for energy production. Information on the regulation and spatial organization of mitochondrial gene expression in the cellular context has been difficult to obtain. Here we addressed this by devising an imaging approach to analyze mitochondrial translation, by following the incorporation of clickable non-canonical amino acids. We applied this method to multiple cell types, including hippocampal neurons, where we found ample evidence for mitochondrial translation in both dendrites and axons. Translation levels were surprisingly heterogeneous, were typically stronger in axons, and were independent of their distance from the cell soma, where mitochondria presumably descent from. Presynaptic mitochondrial translation correlated with local synaptic activity, and blocking mitochondria translation reduced synaptic function. Overall, these findings demonstrate that mitochondrial gene expression in neurons is intimately linked to neuronal function.

56 Spatial analysis of transcriptome changes in porcine endometrium on Day 14 of pregnancy

2019 ◽  
Vol 31 (1) ◽  
pp. 153
Author(s):  
S. Zeng ◽  
S. Bauersachs
Keyword(s):  
Gene Expression Regulation ◽  
Sequence Data ◽  
Differential Expression Analysis ◽  
Cell Communication ◽  
Cell Types ◽  
Endometrial Tissue ◽  
Cell Junction ◽  
Rna Seq ◽  
Tissue Samples ◽  
Rna Integrity

During the conception cycle, the embryo undergoes a series of developmental processes including cell division, cellular reorganization, and oestrogen secretion before attaching to the uterine epithelium. The uterine endometrium is complex and consists of various layers and cell types [i.e. luminal epithelium (LE), glandular epithelium (GE), blood cells (B), and stromal areas (S)]. The objective of this study was to characterise the complex transcriptome changes in porcine endometrium during the time of conceptus attachment with respect to localization in different endometrial cell types. RNA-sequencing (RNA-Seq) was conducted for LE, GE, B, and S samples isolated from endometrial tissue collected on Day 14 of pregnancy and the oestrous cycle, respectively (each group n=4), by laser capture microdissection (PALM LCM microscope, Zeiss, Jena, Germany). Total RNA was isolated (RNA integrity number>6.5) and used for the preparation of 32 RNA-seq libraries (Ovation SoLo RNA-Seq System, NuGEN Technologies, San Carlos, CA, USA). Multiplexed (barcode-tagged) libraries were run on an Illumina HiSEqn 2500 (Illumina, San Diego, CA, USA). The obtained sequence data were analysed with a RNA-Seq data analysis pipeline on a local Galaxy server installation. The resulting read counts were used for statistical analysis in EdgeR to identify differentially expressed genes (DEG). Furthermore, an RNA-seq dataset for complete Day 14 endometrial tissue samples from a previous study was analysed using the same pipeline. A total of 14297 genes were detectable in complete endometria, and 12000, 11903, 11094, and 11933 genes in LE, GE, B, and S, respectively. Differential expression analysis was performed between the pregnant and the cyclic nonpregnant group for each cell type and the complete tissue. The highest number of DEG was found for LE (1410) when compared with GE, B, and S (800, 1216, and 384, respectively). In total, 3262 DEG were obtained for the complete tissue between pregnant and nonpregnant gilts. The DEG were assigned to Gene Ontology (GO) terms to characterise overrepresented functional categories and pathways specific for the individual endometrial compartments. The GO classification revealed that most DEG in LE were involved in cell communication, such as ‘extracellular exosome’, ‘extracellular vesicle’, ‘homeostatic process’, whereas the ‘response to organic substance’ and ‘regulation of cell migration’ categories were enriched in GE. In blood vessels, categories such as ‘membrane-bounded vesicle’, ‘cell junction’, ‘cell development’, ‘cell adhesion’ and ‘blood vessel morphogenesis’ were found as overrepresented, whereas in stromal regions, most DEG were assigned to ‘cell communication’ and ‘secretion’. These results confirmed the hypothesis that conceptus signals induce specific transcriptomic regulations in the endometrial compartments/cell types related to their functions during recognition of pregnancy adding a new level of spatial gene expression regulation to endometrial transcriptome analysis.

scholarly journals Interleukin-1 synergy with phosphoinositide pathway agonists for induction of interleukin-2 gene expression: molecular basis of costimulation.

1990 ◽  
Vol 10 (12) ◽  
pp. 6325-6334 ◽  
Author(s):  
T J Novak ◽  
D Chen ◽  
E V Rothenberg
Keyword(s):  
Gene Expression ◽  
Second Messengers ◽  
Interleukin 1 ◽  
Interleukin 2 ◽  
Calcium Ionophore ◽  
Gene Promoter ◽  
Cell Types ◽  
Regulatory Sequences ◽  
Nf Kappa B ◽  
Phosphoinositide Pathway

The macrophage-derived cytokine interleukin-1 (IL-1) can provide a second signal with antigen to elicit production of interleukin-2 (IL-2) by helper T cells. The pathway(s) involved remains controversial, with protein kinase C and cyclic AMP (cAMP) invoked as possible second messengers. In the murine thymoma EL4.E1, IL-1 could synergize with the phosphoinositide pathway, because the cells made higher levels of IL-2 in the presence of IL-1 than could be induced by phorbol ester plus calcium ionophore alone. IL-1 is unlikely to act through a sustained increase in cAMP in these cells because it did not raise cAMP levels detectably and because IL-1 and forskolin had opposite effects on IL-2 gene expression. Inducible expression of a transfected reporter gene linked to a cloned fragment of the murine IL-2 gene promoter was initially increased by IL-1 costimulation, implying that IL-1 can increase the rate of transcription of IL-2. The minimal promoter elements required for iL-1 responsiveness were located within 321 bp of the IL-2 RNA cap site, and further upstream sequences to -2800 did not modify this response. IL-1 costimulation resulted in enhanced activity of both an inducible NF-kappa B-like factor and one of two distinct AP-1-like factors that bind to IL-2 regulatory sequences. Neither was induced, however, by IL-1 alone. Another AP-1-like factor and NFAT-1, while inducible in other cell types, were expressed constitutively in the EL4.E1 cells and were unaffected by IL-1. These results are discussed in terms of the combinatorial logic of IL-2 gene expression.

scholarly journals Antimitogenic and mitogenic actions of interleukin-1 in diverse cell types are associated with induction of gro gene expression

1991 ◽  
Vol 266 (4) ◽  
pp. 2415-2422
Author(s):  
V V Rangnekar ◽  
S Waheed ◽  
T J Davies ◽  
F G Toback ◽  
V M Rangnekar
Keyword(s):  
Gene Expression ◽  
Interleukin 1 ◽  
Cell Types

scholarly journals intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data

BMC Genomics ◽  
2020 ◽  
Vol 21 (S11) ◽  
Author(s):  
Yingying Cao ◽  
Simo Kitanovski ◽  
Daniel Hoffmann
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
High Throughput Sequencing ◽  
Differential Expression Analysis ◽  
Cell Types ◽  
R Package ◽  
Integrative Approach ◽  
Integrated Analysis ◽  
Data Sets ◽  
Rna Seq

Abstract Background RNA-Seq, the high-throughput sequencing (HT-Seq) of mRNAs, has become an essential tool for characterizing gene expression differences between different cell types and conditions. Gene expression is regulated by several mechanisms, including epigenetically by post-translational histone modifications which can be assessed by ChIP-Seq (Chromatin Immuno-Precipitation Sequencing). As more and more biological samples are analyzed by the combination of ChIP-Seq and RNA-Seq, the integrated analysis of the corresponding data sets becomes, theoretically, a unique option to study gene regulation. However, technically such analyses are still in their infancy. Results Here we introduce intePareto, a computational tool for the integrative analysis of RNA-Seq and ChIP-Seq data. With intePareto we match RNA-Seq and ChIP-Seq data at the level of genes, perform differential expression analysis between biological conditions, and prioritize genes with consistent changes in RNA-Seq and ChIP-Seq data using Pareto optimization. Conclusion intePareto facilitates comprehensive understanding of high dimensional transcriptomic and epigenomic data. Its superiority to a naive differential gene expression analysis with RNA-Seq and available integrative approach is demonstrated by analyzing a public dataset.

scholarly journals Interleukin-1 synergy with phosphoinositide pathway agonists for induction of interleukin-2 gene expression: molecular basis of costimulation

1990 ◽  
Vol 10 (12) ◽  
pp. 6325-6334
Author(s):  
T J Novak ◽  
D Chen ◽  
E V Rothenberg
Keyword(s):  
Gene Expression ◽  
Second Messengers ◽  
Interleukin 1 ◽  
Interleukin 2 ◽  
Calcium Ionophore ◽  
Gene Promoter ◽  
Cell Types ◽  
Regulatory Sequences ◽  
Nf Kappa B ◽  
Phosphoinositide Pathway

The macrophage-derived cytokine interleukin-1 (IL-1) can provide a second signal with antigen to elicit production of interleukin-2 (IL-2) by helper T cells. The pathway(s) involved remains controversial, with protein kinase C and cyclic AMP (cAMP) invoked as possible second messengers. In the murine thymoma EL4.E1, IL-1 could synergize with the phosphoinositide pathway, because the cells made higher levels of IL-2 in the presence of IL-1 than could be induced by phorbol ester plus calcium ionophore alone. IL-1 is unlikely to act through a sustained increase in cAMP in these cells because it did not raise cAMP levels detectably and because IL-1 and forskolin had opposite effects on IL-2 gene expression. Inducible expression of a transfected reporter gene linked to a cloned fragment of the murine IL-2 gene promoter was initially increased by IL-1 costimulation, implying that IL-1 can increase the rate of transcription of IL-2. The minimal promoter elements required for iL-1 responsiveness were located within 321 bp of the IL-2 RNA cap site, and further upstream sequences to -2800 did not modify this response. IL-1 costimulation resulted in enhanced activity of both an inducible NF-kappa B-like factor and one of two distinct AP-1-like factors that bind to IL-2 regulatory sequences. Neither was induced, however, by IL-1 alone. Another AP-1-like factor and NFAT-1, while inducible in other cell types, were expressed constitutively in the EL4.E1 cells and were unaffected by IL-1. These results are discussed in terms of the combinatorial logic of IL-2 gene expression.

scholarly journals Genetic Network Architecture and Environmental Cues Drive Spatial Organization of Phenotypic Division of Labor in Streptomyces coelicolor

mBio ◽  
2021 ◽  
Vol 12 (3) ◽  
Author(s):  
Vineetha M. Zacharia ◽  
Yein Ra ◽  
Catherine Sue ◽  
Elizabeth Alcala ◽  
Jewel N. Reaso ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Architecture ◽  
Spatial Organization ◽  
Streptomyces Coelicolor ◽  
Cell Types ◽  
Antibiotic Biosynthesis ◽  
Developmental Pathway ◽  
Content Type ◽  
Reproductive Structures ◽  
Physiological Gradients

ABSTRACT A number of bacteria are known to differentiate into cells with distinct phenotypic traits during processes such as biofilm formation or the development of reproductive structures. These cell types, by virtue of their specialized functions, embody a division of labor. However, how bacteria build spatial patterns of differentiated cells is not well understood. Here, we examine the factors that drive spatial patterns in divisions of labor in colonies of Streptomyces coelicolor, a multicellular bacterium capable of synthesizing an array of antibiotics and forming complex reproductive structures (e.g., aerial hyphae and spores). Using fluorescent reporters, we demonstrate that the pathways for antibiotic biosynthesis and aerial hypha formation are activated in distinct waves of gene expression that radiate outwards in S. coelicolor colonies. We also show that the spatiotemporal separation of these cell types depends on a key activator in the developmental pathway, AdpA. Importantly, when we manipulated local gradients by growing competing microbes nearby, or through physical disruption, expression in these pathways could be decoupled and/or disordered, respectively. Finally, the normal spatial organization of these cell types was partially restored with the addition of a siderophore, a public good made by these organisms, to the growth medium. Together, these results indicate that spatial divisions of labor in S. coelicolor colonies are determined by a combination of physiological gradients and regulatory network architecture, key factors that also drive patterns of cellular differentiation in multicellular eukaryotic organisms. IMPORTANCE Streptomyces coelicolor is a multicellular bacterium that differentiates into specialized cell types and produces a diverse array of natural products. While much is known about the genetic networks that regulate development and antibiotic biosynthesis in S. coelicolor, what drives the spatial organization of these activities within a colony remains to be explored. By using time-lapse microscopy to monitor gene expression in developmental and antibiotic biosynthesis pathways, we found that expression in these pathways occurs in spatiotemporally separated waves. Normally, expression of the antibiotic biosynthesis pathway preceded expression in the developmental pathway; however, this order was compromised in a mutant lacking a key developmental regulator. Furthermore, when we disrupted the local gradients during S. coelicolor growth, we observed disordered patterns of gene expression within colonies. Together, these results indicate that spatial divisions of labor in S. coelicolor colonies are determined by a combination of regulatory network architecture and physiological gradients.

scholarly journals Impact of negative energy balance on transcriptomic profiles of three endometrial cell types isolated by laser capture microdissection in postpartum dairy cows

2020 ◽  
Author(s):  
Wiruntita Chankeaw ◽  
Sandra Lignier ◽  
Christophe Richard ◽  
Theodoros Ntallaris ◽  
Mariam Raliou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Energy Balance ◽  
Dairy Cows ◽  
Cell Types ◽  
Negative Energy ◽  
Negative Energy Balance ◽  
Specific Response ◽  
Endometrial Cell ◽  
Expression Of Genes ◽  
Constitutive Gene Expression

Abstract Background: In postpartum dairy cows, the energy needs to satisfy high milk production induces a more or less pronounced Negative Energy Balance (NEB) status. NEB associated with fat mobilization impairs reproductive function. This study investigated the specific impact of NEB on gene expression in the three main types of endometrial cells at time planned for insemination and implantation. Endometrial cell types (stromal, glandular and luminal epithelial cells) were isolated by laser micro-dissection allowing the study of constitutive gene expression and their specific response to NEB. Methods: Nine Swedish Red cows receiving a control diet or a mild restricted diet to induce differences of energy balance were categorized into mild (MNEB, n = 5) and severe negative energy balance (SNEB, n = 4). The three endometrial cell types: luminal (LE), glandular (GE) epithelium and stroma (ST) were collected by laser microdissection from endometrial biopsies performed at 80 days postpartum. Results: Transcriptome profiles obtained by RNA sequencing revealed differences in constitutive gene expression between the three cells types and also differences in specific responses related to the severity of NEB. Number of differentially expressed genes between SNEB and MNEB cows was higher in ST than in LE and GE, respectively. SNEB was associated with differential expression of genes related to metabolic processes and embryo-maternal interactions in ST. Under-expression of genes related to cell structure was found in GE whereas genes related to pro-inflammatory pathways were over-expressed. Genes associated to adaptive immunity were under-expressed in LE. Conclusion: The three different main cells types of the endometrium, have very different patterns of gene expression. The severity of NEB after calving is associated with changes in gene expression at time of breeding. Specific alterations in GEs are associated with activation of pro-inflammatory mechanisms. Concomitantly, changes in the expression of genes related to cell to cell interactions and maternal recognition of pregnancy takes place in ST. The combination of these effects possibly altering the uterine environment and embryo maternal interactions may negatively influence the establishment of pregnancy.

scholarly journals Expansion-Assisted Iterative-FISH defines lateral hypothalamus spatio-molecular organization

2021 ◽  
Author(s):  
Yuhan Wang ◽  
Mark Eddison ◽  
Greg Fleishman ◽  
Martin Weigert ◽  
Shengjin Xu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lateral Hypothalamus ◽  
Spatial Organization ◽  
Brain Slices ◽  
Morphological Characteristics ◽  
Cell Types ◽  
Molecular Organization ◽  
Marker Genes ◽  
List Type ◽  
Image Datasets

AbstractDetermining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In SituHybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 µm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine novel spatially and molecularly defined subregions. EASI-FISH also facilitates iterative re-analysis of scRNA-Seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.Highlights-EASI-FISH enables robust gene expression profiling in thick brain slices-A turnkey analysis pipeline for facile analysis of large EASI-FISH image datasets-EASI-FISH reveals novel subregions of the lateral hypothalamus-Identification of rare cell types based on morphological and spatial heterogeneity

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